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/*****************************************************************
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* SQUID - a library of functions for biological sequence analysis
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* Copyright (C) 1992-2002 Washington University School of Medicine
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* This source code is freely distributed under the terms of the
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* GNU General Public License. See the files COPYRIGHT and LICENSE
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*****************************************************************/
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* Globally defines the IUPAC symbols for nucleic acid sequence
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* Slowly evolving into a repository of globals. Tue Apr 20 1993
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* RCS $Id: iupac.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: iupac.c,v 1.3 2001/02/21 21:09:10 eddy Exp)
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/* Default expected nucleotide occurrence frequencies, A/C/G/T.
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* Used (for instance) as the default distribution for
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* i.i.d. random nucleotide sequences.
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float dnafq[4] = { 0.25, 0.25, 0.25, 0.25 };
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/* Dayhoff f(i) amino acid occurrence frequencies.
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* From SwissProt 34: 21,210,388 residues
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* In alphabetic order by single-letter code.
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* Used (for instance) as the default distribution for
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* i.i.d. random protein sequences.
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char aa_alphabet[] = AMINO_ALPHABET;
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/* aa_index converts to pam's 27x27 scheme */
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int aa_index[20] = { 0, 2, 3, 4, 5, 6, 7, 8, 10, 11,
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12, 13, 15, 16, 17, 18, 19, 21, 22, 24 };
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/* IUPAC code translations */
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/* note: sequence chars are UPPER CASE */
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struct iupactype iupac[] = {
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{ 'A', 'T', NTA, NTT, },
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{ 'C', 'G', NTC, NTG, },
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{ 'G', 'C', NTG, NTC, },
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{ 'T', 'A', NTT, NTA, },
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{ 'U', 'A', NTU, NTA, },
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{ 'N', 'N', NTN, NTN, },
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{ ' ', ' ', NTGAP, NTGAP, },
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{ 'R', 'Y', NTR, NTY, },
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{ 'Y', 'R', NTY, NTR, },
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{ 'M', 'K', NTM, NTK, },
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{ 'K', 'M', NTK, NTM, },
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{ 'S', 'S', NTS, NTS, },
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{ 'W', 'W', NTW, NTW, },
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{ 'H', 'D', NTH, NTD, },
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{ 'B', 'V', NTB, NTV, },
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{ 'V', 'B', NTV, NTB, },
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{ 'D', 'H', NTD, NTH, },
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char *stdcode1[65] = {
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char *stdcode3[65] = {
added
removed
src/squid/iupac.c
